July 24, 2008

Cuban mtDNA and Y chromosomes

A message from this study is that Y chromosome diversity within an already settled territory can indeed be wiped out. Introduction of new pathogens or a technological differential between colonists and natives, are just two possible ways to achieve this.

Many technological innovations (e.g. farming, Bronze, Iron) originated in a very small part of the Old World and spread far and wide. I would not be very surprised if this coincided with a massive replacement of Y chromosomes. The legacy of the earlier inhabitants may, of course, endure, via mtDNA, or autosomal DNA.

BMC Evol Biol. 2008 Jul 21;8(1):213. [Epub ahead of print]

Genetic origin, admixture, and asymmetry in maternal and paternal human lineages in Cuba.

ABSTRACT: BACKGROUND: Before the arrival of Europeans to Cuba, the island was inhabited by two Native American groups, the Tainos and the Ciboneys. Most of the present archaeological, linguistic and ancient DNA evidence indicates a South American origin for these populations. In colonial times, Cuban Native American people were replaced by European settlers and slaves from Africa. It is still unknown however, to what extent their genetic pool intermingled with and was 'diluted' by the arrival of newcomers. In order to investigate the demographic processes that gave rise to the current Cuban population, we analyzed the hypervariable region I (HVS-I) and five single nucleotide polymorphisms (SNPs) in the mitochondrial DNA (mtDNA) coding region in 245 individuals, and 40 Y-chromosome SNPs in 132 male individuals. RESULTS: The Native American contribution to present-day Cubans accounted for 33% of the maternal lineages, whereas Africa and Eurasia contributed 45% and 22% of the lineages, respectively. This Native American substrate in Cuba cannot be traced back to a single origin within the American continent, as previously suggested by ancient DNA analyses. Strikingly, no Native American lineages were found for the Y-chromosome, for which the Eurasian and African contributions were around 80% and 20%, respectively. CONCLUSIONS: While the ancestral Native American substrate is still appreciable in the maternal lineages, the extensive process of population admixture in Cuba has left no trace of the paternal Native American lineages, mirroring the strong sexual bias in the admixture processes taking place during colonial times.

28 comments:

How could admixture eliminate Y DNA lineages if Y DNA is thought to be thousands of years old? I don't know anything about Cuban history, but is it possible that the native males were eliminated or died off?

There are African Americans who have a Y Chromosome common to Europe, like R1b and then marry a "white" woman and there kids would look perfectly Europe if you go by Haplogroups, but on an admixture test the kid can be 60% European and 40% African, in America they will likely just be called "black" and might be no lighter than Obama or even darker.

With native males, it is likely that there offspring just had a far less chance of surviving than a European male or even a black slave due to the social structure on the island when Europeans invaded (and death due to disease).

Dean asked, "How could admixture eliminate Y DNA lineages if Y DNA is thought to be thousands of years old?" The Y- lineages may indeed be thousands of years old, but not necessarily in the region in question. Men from a population move in and gradually take over, often having children with local women. If they bring in large numbers of women mtDNA lineages can also be lost.

It's easily possible to interpret the evidence from modern distribution of Y- and mtDNA haplogroups as indicating the process has happened many times throughout history and prehistory. Take note Maju.

How could admixture eliminate Y DNA lineages if Y DNA is thought to be thousands of years old? I don't know anything about Cuban history, but is it possible that the native males were eliminated or died off?

In Cuba at least, the natives were wiped out in few generations, almost regardless of gender. But the mestizos survived and actually made up the backbone of the Spanish colonial empire. All mestizos had European Y-DNA and Native mtDNA since the very beginning: the opposite was not concievable (and anyhow very few European women migrated to America, specially in the first centuries).

The process in the greater antilles is not 100% extrapolable to the mainland though, where some native populations were much more resistent (because of several factors, specially population density).

...in America they will likely just be called "black"...

You mean in the USA, right? In other parts of America they would be called mulatto probably.

It's easily possible to interpret the evidence from modern distribution of Y- and mtDNA haplogroups as indicating the process has happened many times throughout history and prehistory. Take note Maju.

You are telling the tale of a modern nation invading stone age ones (chalcolithic at most) and pouring immigrants across the ocean for four or more centuries (plus the epidemic shock). It's not a circumstance we may expect to have happened often in Eurasia, really.

Indo-European expansion, for instance, has some elements of that probably, but it took several milennia (actually American conquest was just the last stage of it, even if thise IEs had almost not R1a, after many prior stages of "mestizage" and aculturation) and mostly conquered peoples at similar technological level, and at much higher demographic densities.

People look at the conquest of the USA or Australia and think that all was that dramatic in the past. But it was not - it's just impossible that such things happened in most of prehistoric Eurasia. The Spanish conquest of America is a better example surely but still... when have you seen a whole continent succumb to invaders in just 40 years? It would have been impossible if the parties would have been at smilar technological levels and there was no biological shock.

"People look at the conquest of the USA or Australia and think that all was that dramatic in the past... it's just impossible that such things happened in most of prehistoric Eurasia... when have you seen a whole continent succumb to invaders in just 40 years?"

I think you've answered your own question. In prehistoric Eurasia it took a lot longer than just 40 years. In those ancient times technological levels were not exactly the same as each other (just a small advantage can have a huge effect with enough time) and we don't know that "there was no biological shock".

I think it's safe to assume humans haven't changed that much in the last 40,000 or 50,000 years.

By the way. You'll have to excuse Dragon Horse. Years ago I went to a party in Madrid and some Canadians said, "Isn't it amazing. We have 30 people here and not one American." I said, "What do you mean. You're all Americans except me".

In those ancient times technological levels were not exactly the same as each other (just a small advantage can have a huge effect with enough time)...

They were about the same. While Europeans were conquering America and harassing Africa with a handful of adventurers and maybe a cannon or two, they were having huge problems fencing off the Turks and the Algerians, who were roughly the same tech level. Only with the Industrial Revolution did Europeans begin to become really ahead of other Eurasian peoples and became able to defeat them in the battlefield with some ease.

Even then, Indians were not wiped out by the Brits nor Algerians by the French (etc.) It was a totally different situation: even if there was some clear tech advantage on the European side, they were still roughly at the same level. Only the Russian conquest of Siberia resemble somewhat what happened in America. Why? Because of tech difference and specially extremely low population density of the natives.

... and we don't know that "there was no biological shock".

Admitted. But Eurasia and America were separate continents for milennia, linked only by a tiny thread at Bering strait. Illnesses that were common in Eurasia were unknown in America and vice versa. That kind of brutal biological shock could not have happened inside either continent. The common flu could not have been an accidental weapon of mass destruction, as it was not in Africa (for this purpose part of Eurasia - or Eurafrasia if you wish).

Regarding Native Y chromosomes in Cuba (or Colombia and other places in Latin America) being wiped out, part of it is due to the fact that Native women often preferred to marry White (or sometimes Black) men to men of their own kind. Latin American chronicles are full of accounts of Native women leaving Native husbands and pairing up with White men. Teaming up with a White men could bring Native women social privileges, and a mixed-race child would be higher on the social totem pole than one of pure Native descent. So that is probably the principal reason why Native Y chromosomes are reduced or completely eliminated in many Latin American mixed-race populations.

"They were about the same". Now I've hardly ever read anything about the replacement of Neanderthals by modern humans that doesn't argue in favour of some superiority of modern humans. If you can find an example that fails to claim this please let me know. I'd love to see it.

Terry: I have not the slightest idea on why Neanderthals went extinct (nor I care too much: the fact is that they died out - maybe they died out because they were hyper-intelligent and therefore foresaw the horrible future and said: no, thank you). But I know they were not H. sapiens, so it's like comparing apples and oranges. Why do you even bring that up here?

Maju. I was merely pointing out that the European expansion into America has parallels with the modern human expansion into Europe. Many people involved in the European expansion into America argued that the indigeneous inhabitants were hardly human. So it's hardly "like comparing apples and oranges".

If you read any of John Hawks and Greg Cochran's work you would see that since the Neolithic humans have changed a lot - put simply, more humans = more mutations.

But, unless these are clearly adaptative mutations, they are likely to remain restricted. There's much less drift (and therefore virtually no fixation for this reason). Variability has increased for sure with raw numbers but only those really adaptative genes of the kind of the lactose-digesting ones have experienced some sort of consolidation - and an irregular one anyhow.

Bur more people = greater population density = more pathogens, more warfare, more competition of all sorts

The result is massive selection and selective sweeps.

I don't see that. Not at all. Adaptative genes like lactose-tolerance ones may infiltrate (introgression?) some populations but if you can see so many peoples that didn't get that one... well, the impression is that even adaptative alelles are not that "all powerful" - not to mention most other polymorphic genes that are surely neutral or almost so.

There has been not a single massive bottleneck in Western Eurasia since the Neolithic (or probably late UP) so let's not get flippant about "population sweeps", selective or not, let's not build skycrappers on ghostly moving sands, ok?

In other words, we are not our ancestors of 10,000 ya - they are as different from us as they are from much earlier humans.

We are obviously not ever our ancestors: we are a particular combination of some of their genes, not them - never them. But that doesn't mean they are not our ancestors.

"People have probably changed more in the last 10,000 years than in the preceding 100,000 years!" As Maju says, more mutations don't necessarily translate to more evolution. You need selection as well.

My comment "I think it's safe to assume humans haven't changed that much in the last 40,000 or 50,000 years" was made in relation to intertribal interaction and conflict. I'm sure that many of the Australian Aborigines I've met, for example, have received very few genes from outside that continent since long before the Neolithic expansion. Amazingly I had very little trouble communicating with them In English though). Do you believe they've somehow changed in parallel with the remainder of humanity? I'll admit they've undergone a huge level of selection in the last 200 years.

But there is more selection today than any other time in hominid evolution - that my point!

Terry,

I made my comments in reference to Eurasian populations, for other populations - like African or American - there have been less selection as population density was low, due to agriculture starting later.

In some populations, like Australian Aborigines, there are probably different factors at work, like drift - which operates in small populations. However I'm aware that one language group Pama-Nyungan - http://en.wikipedia.org/wiki/Pama-Nyungan_languages - accounts for 95% of all aboriginal languages, ans seems to have spread in only the last 5,000 years or so - so even here there has been some sort of cultural sweep, which may have been mediated by some new technology developed by one group, or the arrival of some new group of people to the continent - with hunting dogs/dingoes for example. In either case, this sweep may have been accompanied by a genetic sweep as well, who knows.

But there is more selection today than any other time in hominid evolution - that my point!

It's a point that is not clear at all. I really don't understand why you claim that, PConroy, but in any case these are my "blind" objections:

As evolutionary pressure decreases because of more secure food resources and, more modernly, improved health care, selection is not happening - at least not the typical biological selection, not as much as it used to. Maybe there is some sort of socio-political selection, like favoring mediocrity and conformism - but that's about all.

Increased diversity is not selection, but a greater genetic pool from where natural selection will be able to choose when there is a major crisis. This crisis has not yet happened, at least not in any major scale. There has been no meaningful bottlenecks since Neolithic began, at least for most peoples in the Old World. The closest I can think of could be epysodes like the Black Death, but even these massive epydemics fell very short of meaning bottleneck, and their genetic selection effect is very unclear.

"so even here there has been some sort of cultural sweep, which may have been mediated by some new technology developed by one group, or the arrival of some new group of people to the continent". I'd totally agree with that.

But. There seems to be no genetic evidence for such arrival so Australian Aborigine genes were little altered from outside. And yet they seem to be much the same as us. If we have greatly changed over the last 50,000 years Australian Aborigines would surely provide us with evidence of the degree of such difference. The fact that near enough to 50,000 years of evolution have not led to very much diversity between Australian Aborigines and Europeans indicates that the evolution in question has been fairly minor.

"People who lived 10,000 years ago were much more like Neanderthals than we are like those people," says John Hawks...

C'mon!

It's all very speculative. Increase in autism and schizophrenia is surely caused by unnatural birthgiving practices, which traumatizes the child heavily and maybe forever, not genetics. How would us evolve in a self-damaging sense? That's not evolution but involution.

We could go on (in fact most of the article talks about isolated cases of genetic engineering in humans). But I'd rather discus Hawks opinions on his own blog when he dares to admit criticism (comments). He seems one of those with the "lightbulb over the head" complex, IMO.

It would seem that genes linked to schizophrenia are actually under positive selection, ditto for autism - the reason being that in the heterozygous state, they confer a cognitive advantage

Not sure for autism, illness I have found less people with through my life, but I have yet to find a direct relative of a schizophrenic who is smart at all. In my experience, schizos may be somewhat smarter and more sensitive at times but their relatives, the ones most likely to have the heterozygotic state, never. They are typically very authoritarian though.

Anyhow, we'll stay tuned for further research. But so far this is stuff of speculation, mostly focused on the vast and slippery terrain of the human psyche - of which only a very little bit is known so far.

Wasn't it recently that some researchers published "complaining" about how poor quality of psychiatric diagnosis hindered genetic research on issues like schizophrenia precisely?

Pconroy. Do Australian Aborigines suffer from schizophrenia or is it only those who have some European ancestry? I'm fairly sure it's not uncommon amoung them. I'm less sure of autism although I tend to suspect autism is developmental rather than being genetic.

But I suppose we could just consider Europeans' evolution rather than looking at the whole of humanity. As I've said elsewhere, it's possible to come up with all sorts of theories about human evolution, but once we take Australian Aborigines into consideration it narrows our options.

but once we take Australian Aborigines into consideration it narrows our options

But as I pointed out earlier, although Australian Aborigines (AAs) differ quite a bit from Eurasians genetically, they may have differed much more so, prior to about 5,000 years ago - as there was a cultural sweep and possibly demographic/genetic sweep also.

Pconroy. Although it is pretty well established that the dingo, and what has been called the pirri point culture, arrived in the north of Australia somewhere around 5000 years ago (probably associated with the Austronesian expansion from Eastern Indonesia) it's universally considered that the genetic contribution to humans already existing on the continent was minimal. There is certainly no evidence of new Y-chromosome or mtDNA haplogroups. Mind you we know that they can be independent of other genes (and this provides an explanation for how Neanderthal genes might survive of course).

The Pama-Nyungan expansion probably originated from around the Murray/Darling basin and presumably represents a recolonisation of the interior after an extreme drought.

I've put some thoughts regarding Australian settlement up at remotecentral. The relevant bit is at the end under "More Evidence".

With regards to the mtDNA/Y-chromosome in Cubans paper, the expatriate, overwhelmingly Caucasian portion of the population was omitted-- one in seven Cubans. Also, 30% Amerindian mtDNA does not mean that the Cuban population is 30% Amerindian genetically. This lack of basic genetics has caused some papers to be published in which the Cuabn genome is incorrectly characterized as 30% Amerindian.

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